The Influence of Anticodon-Codon Interactions and Modified Bases on Codon Usage Bias in Bacteria
The Influence of Anticodon-Codon Interactions and Modified Bases on Codon Usage Bias in Bacteria
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DOI：
10.1093/molbev/msq102
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发表时间：
2010-09-01
影响因子：
10.7
通讯作者：
Higgs, Paul G.
中科院分区：
文献类型：
--
作者：
Ran, Wenqi;Higgs, Paul G.
大多数转运RNA（transfer RNA，tRNA）可以翻译多个同义密码子，大多数密码子可以被多个异源受体tRNA翻译。同义密码子的翻译速率取决于tRNA的浓度和每个反密码子-密码子组合的配对速率。翻译选择导致大多数细菌中高表达基因的密码子频率的显著偏差。通过比较高表达基因和低表达基因中的密码子频率，我们确定了大样本细菌基因组中每个氨基酸的首选密码子。我们将其与每个基因组中每个tRNA基因的拷贝数联系起来。在双密码子家族中，优选的密码子在第三密码子碱基和反密码子的摆动碱基之间具有沃森-克里克对（GC和Au），而不是GU对。这表明这些组合更快地被核糖体识别。相反，在四密码子家族中，优选密码子不符合沃森-克里克规则。在某些情况下，摆动U tRNA可以与所有四个密码子配对。在这些情况下，A和U密码子优于G和C。这表明，非标准UU组合似乎翻译得令人惊讶地好。在反密码子的摆动位置的修改的碱基的差异似乎是负责在两个和四个密码子家族的tRNA的行为的差异。我们讨论了反密码子中碱基的变化对翻译速度和准确性的影响。tRNA基因拷贝的数量和翻译选择的强度与生物体的生长速率相关，正如我们所预期的那样，如果细菌中翻译选择的主要原因是优化蛋白质生产速度的要求。
Most transfer RNAs (tRNAs) can translate more than one synonymous codon, and most codons can be translated by more than one isoacceptor tRNA. The rates of translation of synonymous codons are dependent on the concentrations of the tRNAs and on the rates of pairing of each anticodon-codon combination. Translational selection causes a significant bias in codon frequencies in highly expressed genes in most bacteria. By comparing codon frequencies in high and low-expression genes, we determine which codons are preferred for each amino acid in a large sample of bacterial genomes. We relate this to the number of copies of each tRNA gene in each genome. In two-codon families, preferred codons have Watson-Crick pairs (GC and AU) between the third codon base and the wobble base of the anticodon rather than GU pairs. This suggests that these combinations are more rapidly recognized by the ribosome. In contrast, in four-codon families, preferred codons do not correspond to Watson-Crick rules. In some cases, a wobble-U tRNA can pair with all four codons. In these cases, A and U codons are preferred over G and C. This indicates that the nonstandard UU combination appears to be translated surprisingly well. Differences in modified bases at the wobble position of the anticodon appear to be responsible for the differences in behavior of tRNAs in two- and four-codon families. We discuss the way changes in the bases in the anticodon influence both the speed and the accuracy of translation. The number of tRNA gene copies and the strength of translational selection correlate with the growth rate of the organism, as we would expect if the primary cause of translational selection in bacteria is the requirement to optimize the speed of protein production.